Extended molecular dynamics of a c-kit promoter quadruplex

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F15%3A00086620" target="_blank" >RIV/00216224:14740/15:00086620 - isvavai.cz</a>

Alternative codes found

RIV/68081707:_____/15:00455886

Result on the web

<a href="http://nar.oxfordjournals.org/content/43/18/8673.full.pdf+html" target="_blank" >http://nar.oxfordjournals.org/content/43/18/8673.full.pdf+html</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gkv785" target="_blank" >10.1093/nar/gkv785</a>

Result language

angličtina

Original language name

Extended molecular dynamics of a c-kit promoter quadruplex

Original language description

The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 mu s long, similar to 50 mu s in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal mu s-scale transitions in the loops,which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability.

Czech name

—

Czech description

—

Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CE - Biochemistry

OECD FORD branch

—

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2015

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

—

Volume of the periodical

43

Issue of the periodical within the volume

18

Country of publishing house

GB - UNITED KINGDOM

Number of pages

21

Pages from-to

8673-8693

UT code for WoS article

000366406500014

EID of the result in the Scopus database

—